Cleanup

hms-dbmi · Oct 8, 2024 · 851b4b8 · 851b4b8
1 parent d992e58
commit 851b4b8
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Showing 3 changed files with 7 additions and 12 deletions.
diff --git a/.github/workflows/github-actions-test.yml b/.github/workflows/github-actions-test.yml
@@ -14,6 +14,6 @@ jobs:
           java-version: '21'
           distribution: 'temurin'
       - name: Test with Maven
-        run: mvn clean test
+        run: mvn --update-snapshots test
         env:
           GITHUB_TOKEN: ${{ github.token }}
diff --git a/...ssing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PhenotypeMetaStore.java b/...ssing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PhenotypeMetaStore.java
@@ -22,7 +22,6 @@ public class PhenotypeMetaStore {
     private TreeMap<String, ColumnMeta> metaStore;
 
     private TreeSet<Integer> patientIds;
-    private String columnMetaFile;
 
     public TreeMap<String, ColumnMeta> getMetaStore() {
         return metaStore;
@@ -41,27 +40,24 @@ public ColumnMeta getColumnMeta(String columnName) {
     }
 
     @Autowired
+    @SuppressWarnings("unchecked")
     public PhenotypeMetaStore(@Value("${HPDS_DATA_DIRECTORY:/opt/local/hpds/}") String hpdsDataDirectory) {
-        columnMetaFile = hpdsDataDirectory + "columnMeta.javabin";
-        try (ObjectInputStream objectInputStream = new ObjectInputStream(new GZIPInputStream(new FileInputStream(columnMetaFile)));){
+        String columnMetaFile = hpdsDataDirectory + "columnMeta.javabin";
+        try (ObjectInputStream objectInputStream = new ObjectInputStream(new GZIPInputStream(new FileInputStream(columnMetaFile)))){
             TreeMap<String, ColumnMeta> _metastore = (TreeMap<String, ColumnMeta>) objectInputStream.readObject();
-            log.info("columnMetaFile = " + columnMetaFile);
-            log.info("_metastore.size() = " + _metastore.size());
-            TreeMap<String, ColumnMeta> metastoreScrubbed = new TreeMap<String, ColumnMeta>();
+            TreeMap<String, ColumnMeta> metastoreScrubbed = new TreeMap<>();
             for(Map.Entry<String,ColumnMeta> entry : _metastore.entrySet()) {
                 metastoreScrubbed.put(entry.getKey().replaceAll("\\ufffd",""), entry.getValue());
             }
             metaStore = metastoreScrubbed;
             patientIds = (TreeSet<Integer>) objectInputStream.readObject();
-            log.info("patientIds.size() = " + patientIds.size());
-            objectInputStream.close();
         } catch (IOException | ClassNotFoundException e) {
             log.warn("************************************************");
             log.warn("Could not load metastore", e);
             log.warn("If you meant to include phenotype data of any kind, please check that the file " + columnMetaFile + " exists and is readable by the service.");
             log.warn("************************************************");
-            metaStore = new TreeMap<String, ColumnMeta>();
-            patientIds = new TreeSet<Integer>();
+            metaStore = new TreeMap<>();
+            patientIds = new TreeSet<>();
         }
     }
 

diff --git a/...c/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/AbstractProcessorIntegrationTest.java b/...c/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/AbstractProcessorIntegrationTest.java
@@ -7,7 +7,6 @@
 import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query;
 
 import org.junit.jupiter.api.BeforeAll;
-import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.springframework.beans.factory.annotation.Autowired;